Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays.

Benchmarkingthe performance of complex analytical pipelines is an essential part of developing Lab Developed Assays (LDT). Reference samples and benchmarkcalls published by Genome in a Bottle (GIAB) Consortium have enabled the evaluation of analytical methods. However, the performance of such methods is not uniform across the different regions of the genome/ exomeand different variant typesand lengths. Here we present a scalable and reproducible, cloud-based benchmarkingworkflow that can be used by clinical laboratories to rapidly access and validate the performance of LDT assays, across their regionsof interestand reportable range, using a broad set of benchmarkingsamples.